Submit Data from BaseSpace to NCBI’s Sequence Read Archive

When sequencing data supports a new finding that is reported to the scientific community, it is common practice to share the sequencing data that generated the result, through an archive such as NCBI’s Sequence Read Archive. How would a BaseSpace user do this? Until now, a BaseSpace user would have to download their data locally, and then prepare an SRA submission through NCBI’s published guidelines.

SRA Submission App

Since BaseSpace already stores some of the metadata that go into a submission, we felt we could make this process easier. Today, we’re excited to announce the release of the SRA Submission App, a BaseSpace Labs release. Built in collaboration with NCBI, the app prepares your submission XML and transfers the data directly to SRA from BaseSpace.

Because the SRA asks for metadata that BaseSpace does not know about, the app input form asks for the information needed to complete a submission.


Important note: Users of the app must first register a BioProject and BioSample in order for the submission to be routed correctly.

Upon successful submission, users can expect one email notification from SRA to indicate when they’ve received the data, and a second email with the SRA accession numbers once it has been processed. In case of errors, SRA should send an email indicating the error that may need fixing.

We hope this simplifies the process of submitting BaseSpace data to SRA. If you have questions or comments, please send them to Thanks to Adam Stine and Chris O’Sullivan at SRA for working with us on this!

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.